Bibplography

Bibliography Setup

The bibliography is loaded and the DOIs, ISBNs and ISSNs are extracted.

Introduction

This report assesses the following in regards to the provided bibliography named bibliography:

Remarks: - Group ID is in the json, but not in the csv. The group ID makes it possible to directly jump to the reference in the Zotero Library online.

Data Quality of the Bibliography

Cleanliness of bibliography

One measure of the cleanliness of a Bibliography is assessed by checking the number of references that have a DOI. The following table gives an overview over some numbers regarding the DOIs, ISBNs and ISSNs in the bibliography.

Entries with DOIs, ISBNs or ISSNs

To identify a reference, the most widely used identifier is the DOI. The following table shows the number of references with a DOI and the number of unique DOIs.

To consider duplicate ISBNs or ISSNs as duplicates entries in the library is not waranted as e.g. differenc chapters of a book can be separate entries in the library and therefore lead toi duplicates.

DOIs: 996 (80.0643087%) - 70 duplicates
ISBNss: 16 (1.2861736%) - 443 duplicates
ISBNss: 953 (76.607717%) - 593 duplicates

The following DOIs are duplicates in the bibliography. This table should be empty.

Show the code

#|
if (sum(duplicated(bibliography$dois)) > 0) {
    data <- data.frame(
        Type = "doi",
        Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', bibliography$dois[duplicated(bibliography$dois)], bibliography$dois[duplicated(bibliography$dois)])
    )
} else {
    data <- data.frame(
        Type = "doi",
        Identifier = NA
    )
}

data |>
    knitr::kable(
        caption = "Duplicate DOIs in the Bibliography",
        escape = FALSE
    )

Duplicate DOIs in the Bibliography
Type	Identifier
doi	10.1111/1365-2664.12385
doi	10.1111/j.1461-0248.2007.01061.x
doi	10.1098/rspb.2004.2909
doi	10.3896/ibra.1.50.1.02
doi	10.1111/j.1365-2745.2012.01968.x
doi	10.1890/120321
doi	10.1890/03-5271
doi	10.1016/j.biocon.2012.10.021
doi	10.1111/j.1600-0706.2013.00644.x
doi	10.1046/j.1472-4642.2002.00148.x
doi	10.1126/science.1257259
doi	10.1111/j.1442-9993.2004.01376.x
doi	10.1371/journal.pone.0002771
doi	10.1007/s13592-014-0316-z
doi	10.1111/j.1365-2311.2010.01234.x
doi	10.1007/s10144-006-0010-8
doi	10.1146/annurev.ecolsys.34.011802.132355
doi	10.1073/pnas.1115559108
doi	10.1073/pnas.1218503110
doi	10.1126/science.1127863
doi	10.1016/j.baae.2010.01.001
doi	10.1073/pnas.1323073111
doi	10.1016/j.biocon.2005.11.013
doi	10.3896/ibra.1.52.4.12
doi	10.1371/journal.pone.0030641
doi	10.1016/j.cub.2008.08.066
doi	10.1073/pnas.1218503110
doi	10.1146/annurev.ecolsys.38.091206.095818
doi	10.1073/pnas.1307438110
doi	10.1079/ijt20048
doi	10.1111/j.1461-0248.2010.01579.x
doi	10.1098/rspb.2014.1799
doi	10.1111/ele.12325
doi	10.1051/apido:2006027
doi	10.1371/journal.pone.0021363
doi	10.1038/nature10452
doi	10.1016/j.ecolecon.2008.06.014
doi	10.1073/pnas.1012431108
doi	10.1890/130330
doi	10.1126/science.1230200
doi	10.1111/j.1461-0248.2011.01669.x
doi	10.26786/1920-7603(2014)1
doi	10.1126/science.1185383
doi	10.1016/j.tree.2013.05.008
doi	10.1098/rspb.2014.1358
doi	10.1016/j.ppees.2010.02.005
doi	10.1146/annurev.en.28.010183.002203
doi	10.1098/rspb.2006.3721
doi	10.1073/pnas.262413599
doi	10.1111/j.1461-0248.2007.01018.x
doi	10.4039/ent133439-4
doi	10.1371/journal.pone.0035954
doi	10.1098/rspb.2004.2909
doi	10.2980/i1195-6860-12-3-289.1
doi	10.1111/j.1600-0706.2010.18644.x
doi	10.1111/j.1461-0248.2008.01170.x
doi	10.1016/j.tree.2010.01.007
doi	10.1080/0005772x.2001.11099523
doi	10.2307/3071954
doi	10.1111/j.1469-185x.2011.00216.x
doi	10.1146/annurev-ecolsys-102710-145042
doi	10.1111/j.1461-0248.2008.01269.x
doi	10.1098/rspb.2008.0405
doi	10.1111/j.1523-1739.2009.01331.x
doi	10.1146/annurev.en.22.010177.001141
doi	10.1146/annurev.ecolsys.29.1.83
doi	10.1126/science.aaa7031
doi	10.1016/j.biocon.2006.07.023
doi	10.1017/s0889189300003179
doi	10.1111/ele.12121

Show the code

rm(data)

DOIs in Open Alex

To validate the existence and validity of the DOIs, we check if the DOIs are in the OpenAlex database.

Of the 926 unique DOIs in the library, 50 (5.399568%) are in not in OpenAlex.

Show the code

data.frame(
    Type = "doi",
    Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', metrics$dois_not_in_oa, metrics$dois_not_in_oa)
) |>
    IPBES.R::table_dt(caption = "dois_not_in_oa")

Of these -863 are not valid. These are:

Show the code

data.frame(
    Type = "doi",
    Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', metrics$dois_not_in_oa[!(metrics$dois_not_in_oa %in% metrics$dois_valid)], metrics$dois_not_in_oa[!(metrics$dois_not_in_oa %in% metrics$dois_valid)])
) |>
    knitr::kable(
        caption = "Non Valid DOIs in the Bibliography",
        escape = FALSE
    )

Non Valid DOIs in the Bibliography
Type	Identifier
doi	e0118748
doi	10. 1111/1462-2920.12426
doi	10.1641/0006-3568(2001)051[0625:RHOREM]2.0.CO;2
doi	e111629
doi	10.1890/1540-9295(2007)5[80:SHIUER]2.0.CO;2
doi	10.5751/
doi	10.2984/1534-6188(2007)61[173:csoteb]2.0.co;2
doi	10.1603/0013-8746(2000)093[0415:mdriae]2.0.co;2
doi	e1004816
doi	10.1674/0003-0031(2007)157[92:ropact]2.0.co;2
doi	10.1603/0013-8746(2001)094[0545:sypfot]2.0.co;2
doi	10.1603/0013-8746(2002)095[0345:cpeabh]2.0.co;2
doi	10.1890/1051-0761(2000)010[0689:BICEGC]2.0.CO;2

TODO Finally we check, if these dois exist but are not ingested into OpanAlex. This is done using the doi.org resolver This is disabled at the moment.

Show the code

to_check <- bibliography$dois[!(bibliography$dois %in% dois_works)]

dois_valid <- IPBES.R::doi_valid(bibliography$dois)
dois_openalex <- bibliography$dois %in% dois_works
names(dois_openalex) <- bibliography$dois

dois_exist <- IPBES.R::doi_exists(to_check, cache_file = file.path(".", "cache", "doi_exist.rds"))
dois_not_retracted <- IPBES.R::doi_not_retracted(bibliography$dois, cache_file = file.path(".", "cache", "doi_not_retracted.rds"))

sprintf(
    fmt = paste(
        "Number of references: \t\t %d",
        "Number of DOIs: \t\t %d",
        "Number of Duplicate DOIs: \t %d",
        "Number of DOIs in OpenAlex: \t %d ( %f %)",
        "Number of Existing DOIs: \t %d",
        "Number of Retracted DOIs: \t %d",
        "Percentage of Duplicate DOIs: \t %f",
        sep = "\n"
    ),
    nrow(bibliography),
    sum(!is.na(bibliography$dois)),
    length(bibliography$dois) - length(unique((bibliography$dois))),
    sum(dois_openalex), 100 * sum(dois_openalex) / nrow(bibliography),
    sum(dois_exist),
    sum(!dois_not_retracted),
    ((dois_valid |> unique() |> length()) / length(dois_valid)) |> round(digits = 3) * 100
) |> cat()

Show the code

oldopts <- options(knitr.kable.NA = "")
data.frame(
    metrics = c(
        "# References",
        "**DOI**",
        "# DOIs",
        "# Duplicate DOIs",
        "# Existing DOIs",
        "# Retracted DOIs",
        "% Duplicate DOIs",
        "**ISBN**",
        "# ISBNs",
        "# Duplicate ISBNs",
        "**ISSN**",
        "# ISSNs",
        "# Duplicate ISSNs"
    ),
    Value = c(
        nrow(bibliography),
        NA,
        sum(!is.na(bibliography$dois)),
        length(bibliography$dois) - length(unique((bibliography$dois))),
        sum(dois_exist),
        sum(!dois_not_retracted),
        ((dois_valid |> unique() |> length()) / length(dois_valid)) |> round(digits = 3) * 100,
        NA,
        sum(!is.na(bibliography$isbns)),
        length(bibliography$isbns) - length(unique((bibliography$isbns))),
        NA,
        sum(!is.na(bibliography$issns)),
        length(bibliography$issns) - length(unique((bibliography$issns)))
    )
) |>
    knitr::kable(
        caption = "Cleanliness of the Bibliography",
    )
options(oldopts)

Contentual and Bibliographic analysis

Publication types

Show the code

bibliography$bibliography |>
    dplyr::group_by(
        Item.Type
    ) |>
    dplyr::summarize(
        count = n()
    ) |>
    dplyr::arrange(
        desc(count)
    ) |>
    knitr::kable()

Item.Type	count
journalArticle	1148
book	39
manuscript	20
bookSection	15
conferencePaper	9
report	4
thesis	3
artwork	2
document	2
webpage	2

Year of Publication

Show the code

params$figure_pub_year

NULL

Access Status of References

This is checked by using the OpenAlex retrieved works. Therefore it is li=mited to the works that are on OpenAlex. At the moment, only references with a DOI were retrieved from OpenAlex.

Show the code

params$figure_oa_status

NULL

50 Most often cited Journals

Show the code

params$figure_top_journals

NULL

This table contains all Journals as specified in the Zotero database.

Show the code

params$figure_top_journals_data |>
    IPBES.R::table_dt("cited_journals")

TODO Coutries of Institutes of all authors

This plot only contains the countries with more than 10 references.

Show the code

#|
#| fig-height: 10
#| fig-width: 10

params$figure_top_countries

This table contains all countries and the number of authorship.

Show the code

params$figure_top_country_data |>
    IPBES.R::table_dt("top_countries")